exam 2 Flashcards
1
Q
DNA Strand
A
- written 5’ to 3’
- has bases: guanine, adenine, thymine, cytosine
- polar ends
2
Q
which bond pairs bases?
A
hydrogen bonds
noncovalent
attracted through electronegativity
3
Q
base pairs
A
A + T = adenine + thymine
- only 2 hydrogen bonds
G + C = guanine + cytosine
- 3 hydrogen bonds, strongest
4
Q
purines
A
A and G (pure as gold)
- have two rings
- pair with pyrimidines
5
Q
why can’t G bond with T?
A
oxygens can not bind
6
Q
if the human genome is 30% adenine, how much percentage is it cytosine?
A
20%
- 30 and 30 of A and T
40 of C + G, so 40/2 = 20
7
Q
DNA is double stranded
A
- has 2 polynucleotide chains that are held together by hydrogen bonds
- bases are inward
8
Q
what kind of backbone does DNA have?
A
sugar-phosphate
- energetically favored
9
Q
is the backbone hydrophilic or hydrophobic?
A
hydropillic! bases are hydrophobic
10
Q
what happens if you pair a purine with a purine? pyrimidine with pyrimidine?
A
width is altered
11
Q
DNA strand parallel?
A
yes! needs to be antiparallel for pairing to occur
12
Q
what form is DNA?
A
helix
- takes ten pairs for a complete turn
- energetically favorable
13
Q
what forces support the structure?
A
van der waals
14
Q
where is information found in DNA?
A
encoded in order of nucleotides
- A, C, T, G
- biological alphabet
15
Q
what is different in sequences?
A
different messages
- look the same but say different things
16
Q
DNA packaging
A
3 billion base pairs in 2 meters of DNA
17
Q
how are the 2 meters of DNA packed?
A
chromosomes
18
Q
how many pairs of chromosomes?
A
23 in somatic cells
- not reproductive
- each pair is inherited
19
Q
what is genome?
A
genetic info in chromosomes
20
Q
what is DNA wrapped around with?
A
histone - protein
- reduces length by 1/3rd
21
Q
what is a histone complex called?
A
nucleosome - 8 histone wrapped molecules, 147 pairs
22
Q
what is the charge of histones?
A
positively charge proportion of amino acids - 4 histones
23
Q
what is chromatin?
A
nucleosomes packed on top of one another
24
Q
shape of chromatin?
A
folded loops
25
what do chromatin loops turn into?
chromosomes - stops packaging
26
why is there a lot of lysine and arginine in histones?
they enable histones to bind to sugar phosphate backbone
27
why do chromatins change in structure?
to allow gene response
28
what is used to loosen up DNA?
ATP energy - push to histone octamer
29
what happens to DNA with the complex?
DNA is less accessible
30
what are histone tails?
- play an important role in chromatin structure
- end that sticks out in N-Terminal
31
how are tails modified?
chemical groups
32
why is DNA replication necessary?
need to replace dead cells - lose about 10 to the eleventh cells per year (about mass of body weight)
33
what is DNA replication used for?
growing - embryonic development - growing in children and adolescents - immune response w/ proliferation of B-cell w/ antibody
34
what does it mean for DNA to be semiconservative?
each parent strand is the template for the mew strand which is a complement
35
DNA mechanism
1. unwind helix to make template strands
2. new nucleotides form base pairs with template - link 5' to 3'
36
what way should DNA always go?
ALWAYS 5' TO 3'
37
origin of replication
- begins replication
- initiator proteins recognize unique DNA sequences
38
which bases are highly seen in ORI?
A and T - easier to remove due to less hydrogen bonding
39
how many ORIs are there?
MANY
40
what direction is ORI?
bidirectional - proceed from replication fork
bubbles get larger and larger
41
ORI in e-coli?
DNA is unwound and proceeds in both directions
42
what does helicase do?
separates 2 strands of DNA + is the 1st replication enzyme
- unwinds DNA + breaks hydrogen bonds
43
single strand branding proteins
prevent H-Bonds from reforming
44
what is torsional stress?
super coiling -> rope is twisting on itself
45
topoisomere
create breaks (phosphodiester bonds) to relieve torsional stress
46
what does replication begin with?
primer -> shorter RNA sequence
primer = complimentary to DNA template (ribose sugar, uracil instead of thymine)
47
primase
synthesizes short sequence
48
why cant DNA polymerase synthesize DNA?
needs primer + bind
49
what does the sliding clamp do?
maintains DNA polymerases association with template
50
which way is DNA read? grow?
read 5' to 3', grows 3' to 5'
51
what does polymerase do?
catalyzes condensation reactions
- add nucleotides through formation of phosphodiester bonds
52
how does DNA polymerase extend?
from primer until previous primer - gaps w/ no phosphodiester linkages
53
leading strand
go forward
54
lagging
go back w/ okazaki
55
are lagging and leading related?
yes, coupled -> replication of strand w/ discontinuous synthesis
56
what does nuclease do?
remove RNA primer
57
final polymerase step
fills gaps - complementary DNA
57
what does ligase at end do?
seals gap by forming phosphodiester linkages through discontinuous strands
58
how many base pairs are lost w/ cell division?
70-100
- lagging strand is incompletely replicated
59
telomerase
- reverse transcription - DNA from RNA
60
when is telomerase active?
development + stem cells
61
what happens to repeats?
slowly eaten away
62
telomerase as buffer
protects internal chromosome region
- combines w/ end that can't replicate
63
telomere
repetitive sequence @ ends of linear chromosomes that act as buffer
64
small genetic change
- base pair chnages - gain genes
- helps with evolutions
65
harmful mutations
can cause diseases - cancer, inheritable genetic diseases (sickle cell, huntingtons), cystic fibrosis (multiple mutations)
65
silent mutations
have no effect - in non coding + no chnage in proteins
66
what happens to damage during DNA replication?
proofreading ability of DNA polymerases corrects it
67
how many sites does DNA polymerase proofreading have
have 2 active sites - editing + polymerizing
68
how do incorrect nucleotides fall off?
polymerase bonds loosely and has to change conformation to catalyze phosphodiester bonds
69
what happens when an incorrect nucleotide is added?
newly synthesized DNA unpairs
3' moves into editing -> cannot edit with 3' to 5'
70
where does most of damage come from?
reactive chemicals - produced in cell metabolism
environmental -> uv light, radiation, toxic chemicals
71
what do protein machines do?
scan DNA damage - most is temporary
72
how does a double helix help in repair?
has 2 copies of genetic info
when one is damaged, the other serves as a source
73
what does damage create?
structures not seen in DNA
if it is not fixed b4 replication, there is permanent damage
74
1st step of DNA repair mechanism
damage is recognized + excised by nucleases
75
2nd step of DNA repair mechanism
repair DNA polymerase binds to 3' hydroxyl
- fills in the missing nucleotide using undamaged DNA template
76
3rd step of DNA repair mechanism
ligase seals nick in helix
77
what is mismatch repair?
bases that are not complementary
78
how do you predict the cell determines it needs to make a correction?
look for nicks
79
depurination
guanine + adenine are removed spontaneuously
80
deamination
cytosine is deaminated - removed and produces uracil
adenine is deaminated - produces hypoxanthine and pairs with cytosine
81
if C is deaminated, what would be the sequence of GCAT after a second replication?
GTAT - first = CUTA then GTAT
82
what happens after UV damage?
- pyrimidine dimers
- thymine absorbs UV and becomes reactive w/ adjacent thymine
83
what is the effect of dimers?
polymerase cannot read through dimers
- causes distortion in backbone that is recognized by repair proteins
84
repaired dimers
90% of dimers are repaired in minutes
85
nonhomologous end joining
cells try to repair before 2 fragments drift
- error prone process bc nucleotides can be lost
86
homologous recombination
homologous DNA is the template for DNA
ONLY if break is right after replication
- error free process
87
what causes nonhomologous breaks?
caused by replication fork (chemical assaults)
- no mechanism to replace info
- cells try to quickly repair before 2 fragments drift
88
what does nuclease do in nonhomologous end joining?
clean up ends
89
what does ligase do in nhej?
joins ends
90
what is homologous recombination?
only happens after replication
- one of the broken 3' ends invades homologous DNA duplex -> looking for complementary sequence
91
what happens to the invading strand in HR?
invading strand = elongated by repair polymerase
92
what is PCR used for?
amplify small DNA segments - molecular photocopying
- need significant amounts of DNA
can also detect virus, study genome, diagnosis
93
what is needed to replicate DNA?
template sequence
way to separate double stranded DNA (heat)
primers (dont need primase, nuclease, ligase)
enzymes (polymerase)
nucleotides
94
primers
single stranded - written 5' to 3'
95
reverse primers
at end of 3' to 5' strand - complements
written backwards from 5' to 3'
96
pcr steps
1. heat to break double strand
2. anneal (cool down) - primer w/ complement base pair
3. polymerase in synthesis - extension
97
amplifying gene
lyse cells isolate genomic DNA
98
do primers become amplified in DNA?
yes, bc primers are DNA
99
agarose gel electrophoresis
gel - with negative + positive end
DNA has negative charge
longer would be @ top
100
what are plasmids?
can replicate independently of chromosomes - small circular double-stranded DNA
101
what are plasmids used for
manipulation of genes - can be inserted in amplified gene
102
restriction enzymes
ancient bacterial defense - protect against invading bacteriophages
cleave viral DNA - used in labs + need ligase to join
103
how are PCR and plasmid cut?
restriction enzyme + ligate
104
DNA cloning
1. PCR sequence - contain proper restriction enzyme sites
2. digest backbone w/ same enzyme
3. ligate in test tube w/ vector
4. transform into bacteria
105
DNA sequencing
determines order of nucelotides
106
sanger sequencing
used for smaller pieces of DNA
- added like in PCR (fluorescently labeled)
- fragments are separated by size (capillary gel)
